For me, even if aiba.wufoo.com and wufoo.com/aiba point to the same IP address and have the same functionality, the former feels more like my site, whereas the latter feels more like my part of someone else's site. If you want to create a service that gives people their own presence on the web, this could make a difference.

Alternatively, maybe most users don't pay attention to URLs or look at the distinction above in the same way we developers do.

Also, the subdomain strategy seems to have worked well for Blogger. They serve users' pages from *.blogspot.com, and their own pages from *.blogger.com.